In theory if it is performance related bonus and payrise, then she should be assessed on her performance for the period of the year she was in attendance, and then the bonus and rise pro-rated. So if she was working for 35% of the "performance year", then she should get 35% of the bonus that would be payable to some one who had performed to her level for the whole year.
That is the theory for how an an equal opportunities focussed company shoud work it, but it will depend on the company.
Has she checked her company policies on maternity rights and bonus arrangements? It might be in there but not being kept to.
Depending on how brave she is and how adamant she is that whe deserves it and will fight for it, she could go and talk to HR about how they came to the decision and calmly use the theory above to demonstrate what she feels she has contributed and should be offered.